The annoying thing here is that to "do the right thing" Cabal would need to distinguish bird-track style literate files (hscolour -lit) from tex style (hscolour -lit-tex). I don't think this is reasonable.
I've fixed hscolour - from the newly release version 1.14 there is now no difference between the -lit and -lit-tex options. Both will deal with either style of literate input.
It might be worth asking if hscolour should by default just do the right thing, ie use -lit on .lhs input files.
Hscolour-1.14 also makes this fix. If your source file name ends in .lhs or .ly or .lx, it will be automatically processed with -lit. You can override the guess, by using an explicit -nolit (or -lit) to force the particular behaviour you want. Another new change, is that you can now supply multiple filenames as input, and their colourised contents will be concatenated to the output. Regards, Malcolm